Genetic Variant UGT2B7:p.Pro267Pro (chr4-69098619-A-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001074.4(UGT2B7):c.801A>T(p.Pro267Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 1,610,220 control chromosomes in the GnomAD database, including 209,131 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.58 ( 25991 hom., cov: 30)

Exomes 𝑓: 0.49 ( 183140 hom. )

Consequence

UGT2B7
NM_001074.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.613

Publications

33 publications found

Variant links:

Genes affected

UGT2B7 (HGNC:12554): (UDP glucuronosyltransferase family 2 member B7) The protein encoded by this gene belongs to the UDP-glycosyltransferase (UGT) family. UGTs serve a major role in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This protein is localized in the microsome membrane, and has unique specificity for 3,4-catechol estrogens and estriol, suggesting that it may play an important role in regulating the level and activity of these potent estrogen metabolites. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2017]

UGT2B7 links:

ENSG00000299782 (HGNC:):

ENSG00000299782 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP7

Synonymous conserved (PhyloP=-0.613 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B7	NM_001074.4 link	c.801A>T	p.Pro267Pro	synonymous_variant	Exon 2 of 6	ENST00000305231.12	NP_001065.2	P16662
UGT2B7	NM_001330719.2 link	c.801A>T	p.Pro267Pro	synonymous_variant	Exon 2 of 5		NP_001317648.1	P16662E9PBP8
UGT2B7	NM_001349568.2 link	c.54A>T	p.Pro18Pro	synonymous_variant	Exon 3 of 7		NP_001336497.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B7	ENST00000305231.12 link	c.801A>T	p.Pro267Pro	synonymous_variant	Exon 2 of 6	1	NM_001074.4	ENSP00000304811.7		P16662

Frequencies

GnomAD3 genomes

AF:

0.575

AC:

86867

AN:

150948

Hom.:

25945

Cov.:

show subpopulations

Gnomad AFR

AF:

0.712

Gnomad AMI

AF:

0.485

Gnomad AMR

AF:

0.659

Gnomad ASJ

AF:

0.512

Gnomad EAS

AF:

0.698

Gnomad SAS

AF:

0.603

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.468

Gnomad OTH

AF:

0.586

GnomAD2 exomes

AF:

0.564

AC:

140796

AN:

249522

AF XY:

0.554

show subpopulations

Gnomad AFR exome

AF:

0.714

Gnomad AMR exome

AF:

0.720

Gnomad ASJ exome

AF:

0.508

Gnomad EAS exome

AF:

0.704

Gnomad FIN exome

AF:

0.583

Gnomad NFE exome

AF:

0.475

Gnomad OTH exome

AF:

0.539

GnomAD4 exome

AF:

0.494

AC:

720449

AN:

1459152

Hom.:

183140

Cov.:

AF XY:

0.495

AC XY:

359018

AN XY:

725794

show subpopulations

African (AFR)

AF:

0.716

AC:

23823

AN:

33292

American (AMR)

AF:

0.713

AC:

31682

AN:

44464

Ashkenazi Jewish (ASJ)

AF:

0.509

AC:

13264

AN:

26054

East Asian (EAS)

AF:

0.703

AC:

27819

AN:

39564

South Asian (SAS)

AF:

0.567

AC:

48646

AN:

85794

European-Finnish (FIN)

AF:

0.578

AC:

30865

AN:

53388

Middle Eastern (MID)

AF:

0.527

AC:

3036

AN:

5760

European-Non Finnish (NFE)

AF:

0.459

AC:

510136

AN:

1110556

Other (OTH)

AF:

0.517

AC:

31178

AN:

60280

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

20554

41108

61662

82216

102770

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.576

AC:

86968

AN:

151068

Hom.:

25991

Cov.:

AF XY:

0.584

AC XY:

43107

AN XY:

73760

show subpopulations

African (AFR)

AF:

0.712

AC:

29284

AN:

41148

American (AMR)

AF:

0.659

AC:

10012

AN:

15184

Ashkenazi Jewish (ASJ)

AF:

0.512

AC:

1769

AN:

3454

East Asian (EAS)

AF:

0.697

AC:

3542

AN:

5080

South Asian (SAS)

AF:

0.604

AC:

2897

AN:

4800

European-Finnish (FIN)

AF:

0.573

AC:

5994

AN:

10454

Middle Eastern (MID)

AF:

0.581

AC:

165

AN:

284

European-Non Finnish (NFE)

AF:

0.468

AC:

31635

AN:

67658

Other (OTH)

AF:

0.586

AC:

1231

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1754

3508

5263

7017

8771

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.497

Hom.:

6217

Bravo

AF:

0.590

Asia WGS

AF:

0.655

AC:

2275

AN:

3478

EpiCase

AF:

0.490

EpiControl

AF:

0.481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.42

(source)

DANN

Benign

0.60

PhyloP100

-0.61

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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4-69098619-A-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over